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2018-12-31express: new version, use tags and fix gcc@6.0.0: (#10230)George Hartzell2-4/+30
* express: new version, use tags and fix gcc@6.0.0: Express fails to build with gcc@6.0.0:. The debian project [has a fix](https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811859) but they don't seem to have pushed it upstream. I've opened an issue and a PR in eXpress repo, but eXpress isn't actively developed, so I'm fixing it here too. Since the Spack package was created, the eXpress team tagged their releases. I've updated the package to use the tags. Version 1.5.1 used to be known as 2015-11-29 (same commit). 1.5.2 is new(er). * Make flake8 happ{y,ier}
2018-12-31aspell builds with newer gcc's (#10227)George Hartzell2-0/+38
Apply fix from aspell issue (519) for a pointer dereference bug that newer versions of gcc won't let slip past. There hasn't been a release that includes the fix, this applies the change to the latest release.
2018-12-31fastx-toolkit builds with newer gcc's (#10228)George Hartzell2-1/+13
There's a missing break in a switch statement that newer gcc's dislike. Our #4696 simply disallowed newer gcc's. This fixes the problem instead. It's been [PR'ed upstream](https://github.com/agordon/fastx_toolkit/pull/22). Tested with gcc@5.5.0 and gcc@8.2.0 on CentOS.
2018-12-31bamutil builds with newer gcc's (#10229)George Hartzell5-0/+100
The most recent release of bamutil that we support uses an embedded copy of libStatGen that has several issues that keep it from building with newer releases of gcc. They've all been fixed upstream and the latest release of bamutil would pick them up if/when we support it. The build process has changed though, plus my team needs *this* version. This commit backports those fixes.
2018-12-31ds: new package at 9.8.0 (#9852)Justin Stanley1-0/+58
* ds: new package at 9.8.0rc6 * ds: move patches to patch func * ds: use built-in configure phase, remove autoreconf skip * ds: revert to stable 9.8.0 * ds: remove unnecessary dep types * ds: make url consistent with versions
2018-12-31flang, llvm, pgmath: Add release for 2018-09-21 (#10224)Gary Klimowicz3-0/+21
2018-12-31py-sphinxautomodapi: new python package (#10226)Geoffrey Oxberry1-0/+18
2018-12-30Over specifying Quantum Espresso compiler variables causes problems in some ↵Nichols A. Romero1-6/+13
corner cases. (#10216)
2018-12-30xgboost: make sure "libxgboost.so" is provided under prefix/lib (#10208)Sinan1-0/+7
2018-12-30dealii: workaround concretization issue with PETSc (#10217)Denis Davydov1-1/+3
2018-12-30patches: clean up patch.py, directives, and package class propertiesTodd Gamblin1-4/+2
- cleanup patch.py: - make patch.py constructors more understandable - loosen coupling of patch.py with package - in Package: make package_dir, module, and namespace class properties - These were previously instance properties and couldn't be called from directives, e.g. in patch.create() - make them class properties so that they can be used in class definition - also add some instance properties to delegate to class properties so that prior usage on Package objects still works
2018-12-29Always build glib with iconv (#10219)George Hartzell1-6/+2
* Always build glib with iconv My early PR, #10165, which added a variant to configure glib to use libiconv and defaulted to false, seems to be causing more trouble than the knob is worth. This changes the glib package to always depend on and use libiconv. * libiconv depends_on is no longer conditional
2018-12-28Add GDAL 2.4.0 (#10215)Adam J. Stewart1-2/+8
2018-12-28salmon: Add version 0.12.0 (#10211)Eric1-0/+1
2018-12-28velvet: Add missing zlib dependency to fix installation errors (#10212)Eric1-0/+2
2018-12-28py-testinfra: Add version 1.18.0 (#10210)Eric1-0/+1
2018-12-27Add new versions of optional-lite and string-view-lite (#10179)Andrew Gaspar2-0/+3
2018-12-27xgboost: new package at 0.81 (#9854)Justin Stanley1-0/+22
2018-12-26fix moab installation for version 5.0.2 removed from ftp (#10201)Lukasz1-1/+11
* moab install from git repository, fix version 5.0.2 removed from ftp server * add moab dependencies above verson 5.0.1
2018-12-26Add Stata package (#10189)StackKorora1-0/+104
* First draft for installing Stata 15 I've tested this works on my systems and gives a successful install of STATA 15. * Flake8 cleanup * Another Flake8 * Update license header * Various improvements A lot of improvements as suggested by @adamjstewart * flake8 check
2018-12-26pgmath: depend on awk (#10200)Christoph Junghans1-0/+1
2018-12-26Fix pkgconf downloads (#10202)Adam J. Stewart1-1/+1
2018-12-26Fix libxml2+python and libxslt+python import tests (#10196)Adam J. Stewart2-2/+4
* Fix libxml2+python import tests * Same for libxslt package
2018-12-26mawk: added 1.3.4_p20171017 (#10197)Christoph Junghans1-0/+1
2018-12-26slepc: fix homepage URL (#10199)Satish Balay1-1/+1
2018-12-24dealii: fix build with some Intel compilers (#10188)Denis Davydov1-0/+6
2018-12-24Add latest version of NCCL (#10194)Adam J. Stewart1-3/+3
2018-12-24Add PyTorch 1.0 (#10193)Adam J. Stewart1-2/+4
2018-12-24manta: Add version 1.5.0 and add missing zlib dependency (#10178)Eric1-4/+6
2018-12-23xsdk-0.4.0: add/update package versions: (#10038)Satish Balay4-15/+57
* xsdk-0.4.0: add/update package versions: hypre@2.15.1 mfem@3.4.0 superlu-dist@6.1.0 trilinos@12.14.0-rc1 petsc@3.10.3 dealii@9.0.1 pflotran@xsdk-0.4.0 alquimia@xsdk-0.4.0 sundials@3.2.1 plasma@18.11.1 magma@2.4.0 amrex@18.10.1 slepc@3.10.1 omega-h@9.19.1 strumpack@3.1.1 pumi@2.2.0 tasmanian@6.0 phist@1.7.5 dtk-3.0 [via trilinos features '+dtk+intrepid2+shards'] add option to disable omega-h build [wrt gcc-8 conflict] spack install xsdk~omega-h add option to disable dealii build [wrt cori build error] spack install xsdk~dealii * trilinos: default version should be the prior release
2018-12-23py-cftime: new package (#10066)Neil Flood1-0/+21
* py-cftime: new package * Added dependency on py-setuptools, and version range for py-cython, thanks to the ever-vigilant @adamjstewart
2018-12-23openFOAM-paraview-catalyst (#10129)Simone Bnà6-60/+1176
* paraview: adding variants to use external packages as internal do not compile * paraview: add latest paraview version * catalyst: fixed libvtkexpat undefined reference linking error in Catalyst 5.5 * catalyst: add latest catalyst version * catalyst: added ParaView_DIR env variable to catalyst module * add paraview, catalyst patches - https://gitlab.kitware.com/vtk/vtk-m/merge_requests/1166 - https://gitlab.kitware.com/paraview/paraview/merge_requests/2433 - https://gitlab.kitware.com/paraview/paraview/merge_requests/2436 * - Handle updated library paths for catalyst. Versions 5.4 and old places libraries under a paraview subdirectory. Eg, "lib/paraview-5.4", they are now placed directly under "lib" - Minor code style cleanup * Handle update library and python paths for ParaView-5.5 * catalyst: added ParaView_DIR path to spack_env * BUG: applied the patch to the extracted catalyst source files * paraview: added missing self to a member variable * paraview: added Paraview_DIR to env * catalyst: added osmesa variant * of-catalyst: added new package * add (FOAM,WM)_PROJECT_DIR also to spack_env environment * depends on first openfoam release supporting catalyst * openfoam-com: added missing env variables to module generation * openfoam: fixed flake8 errors * of-catalyst: added full variant and openfoam version dependency * paraview: adding variants to use external packages as internal do not compile * catalyst: fixed libvtkexpat undefined reference linking error in Catalyst 5.5 * catalyst: added ParaView_DIR env variable to catalyst module * add paraview, catalyst patches - https://gitlab.kitware.com/vtk/vtk-m/merge_requests/1166 - https://gitlab.kitware.com/paraview/paraview/merge_requests/2433 - https://gitlab.kitware.com/paraview/paraview/merge_requests/2436 * - Handle updated library paths for catalyst. Versions 5.4 and old places libraries under a paraview subdirectory. Eg, "lib/paraview-5.4", they are now placed directly under "lib" - Minor code style cleanup * Handle update library and python paths for ParaView-5.5 * catalyst: added ParaView_DIR path to spack_env * BUG: applied the patch to the extracted catalyst source files * of-catalyst: added new package * add (FOAM,WM)_PROJECT_DIR also to spack_env environment * depends on first openfoam release supporting catalyst * paraview: added missing self to a member variable * openfoam-com: added missing env variables to module generation * openfoam: fixed flake8 errors * paraview: added Paraview_DIR to env * catalyst: added osmesa variant * of-catalyst: added full variant and openfoam version dependency * paraview-catalyst: use always external expat and netcdf * of-catalyst: reformatted package description * paraview-catalyst: removed duplicated function * catalyst: fixed flake8 error * of-catalyst: fixed license header * of-catalyst: minor changes * of-catalyst: renamed gitrepo with git * of-catalyst: removed useless gitrepo parameter
2018-12-23Feature add breathe and m2r (#10180)Brian Van Essen3-0/+61
* Added a package for the MDAnalysis toolkit. * Added python packages for breathe and m2r. Updated versions and URL for the sphinx package. * Fixed flake8 error * Updated package requirements based on feedback. * Updated with requirements from the setup.py * Switched it back to pypi.
2018-12-23py-pynio: new package (#10074)Neil Flood1-0/+71
* py-pynio: new package * Major re-working to add some of the optional dependencies, and make it conform to the approach described in the pynio setup.py comments. Much of it turned out to be too complicated, and I have added some notes in comments to explain this to future adventurers. * Added variants for the hdf5 and gdal dependencies, which do seem to be genuinely optional. Also added absolute dependencies for jpeg and zlib, which setup.py says it wants, but were being found as the os-installed versions. * Added descriptions for the new variants, and moved them to above the dependencies
2018-12-22Add missing module env variable setting causing OSS to fail. (#10182)Jim Galarowicz1-0/+11
2018-12-22r-corhmm: new package at 1.22 (#9859)Justin Stanley1-0/+31
2018-12-22petsc-3.10.3: syncs with superlu-dist-6.1. (#10166)Satish Balay1-2/+6
2018-12-21gpgme: new package (#10174)Levi Baber1-0/+19
2018-12-21add charliecloud 0.9.6 (#10176)Jordan Ogas1-0/+1
2018-12-21py-numba: fix py-llvmlite version (#10175)Matthias Wolf1-1/+1
2018-12-21Add libiconv variant to glib (#10165)George Hartzell1-0/+6
Enable explicitly building glib with or without libiconv. Heads up: if you build with ~iconv but there is something else in the spec that includes libiconv then glib will *still* automagically discover it and the build will fail.
2018-12-20R3D spackage (#10164)Daryl W. Grunau1-0/+49
* r3d spackage * address Adam's review comments * fix flake8: too many blank lines
2018-12-20update h5py to 2.9.0 (#10169)Sajid Ali1-1/+2
* modified: var/spack/repos/builtin/packages/py-h5py/package.py * Update package.py * Update package.py
2018-12-20Update TFEL package (#9995)thelfer1-6/+39
* add the tfel package * fix the tfel package * fix the tfel package * fix the tfel package * Taking Adam J. Steward' remarks into account * fixes trailing white spaces * Update description * Update dependencies following @adamjstewart adices * Style fixes * Style fixes * Add java optional support * add the maintainers attribute (following @alalazo advice), disable interface not selected (following @adamjstewart advice) * flake8 fixes * Fix Cast3M and python-bindings support. Python detection is made compatible with cmake'FindPythonLibs module (at least how it is used in TFEL) * Style fixes * Style fixes * Fix test on python version * Follow @adamjstewart advices: code is much cleaner and readable * Small fix * Small fix * Add comment * Small fix in cmake option * try again (trying to overcome Travis CI unstable build process)
2018-12-20OpenFOAM-v1812 - new version (#10167)Mark Olesen1-0/+2
2018-12-20packages/phist: add maintainer (#10162)jthies1-0/+2
2018-12-19CGNS: Allow use of git branch versions (#10156)Greg Sjaardema1-0/+3
* CGNS: Allow use of git branch versions Add ability to use git `master` and `develop` branches of the CGNS library. The `seacas` package sometimes needs to use the `master` or `develop` branch due to some new changes to the parallel I/O implementation in CGNS which has not yet been released. * CGNS: Reorder to put newest version on top Based on review comments, place newest version (develop) first in list.
2018-12-19dyninst: patch to build dyninst with older gcc (#10160)Mark W. Krentel2-0/+74
* dyninst: patch to build dyninst with older gcc Add 'v9.3.2-auto.patch'. This patch changes some 'auto t: type' usage to the older but equivalent 'type.begin()'. This allows building dyninst 9.3.2 with gcc 4.4 which doesn't support the newer syntax. This patch is harmless with newer gcc. * Fix typo in patch. (My bad for sloppy cut-and-paste.) * Restrict the patch to gcc 4.7 and earlier. gcc 4.8 supports the newer usage and thus doesn't need the patch.
2018-12-19sqlite: add 3.26.0 (#10138)Michael Kuhn3-90/+4
2018-12-19updated checksum for kallisto (#10158)Owen Solberg1-1/+1
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